An atomic interaction energy approach to the reactivity of the aromatic ring toward electrophilic attack

A procedure of constructing a complete fragment orbital basis set is described in detail. It provides a complete fragment orbital basis for PMO analysis of the atomic interaction energy. Rt values, a ratio of the bonded atomic interaction energy to the nonbonded interaction energy arising from the peripheral atoms of the aromatic rings, indicate a decrease in the reactivity of the aromatic ring toward electrophilic attack in the sequence: pyrrole > imidazole > furan > pyrazine > pyrimidine > aniline > benzene > pyridine > p-acylaniline > p-cyanoaniline > p-nitroaniline > m-cyanoaniline. © 1995 John Wiley & Sons, Inc.     

Coordination properties of (chloro)aluminum-5,15-diphenyloctaalkylporphyrin in the reactions with small organic molecules

The reactions of aluminum porphyrinate ((Cl)AIP) with organic molecules L (imidazole, pyridine, pyrimidine, and pyrazine) in benzene were studied using spectral and quantum-chemical methods. The structures and stabilities of the molecular complexes (Cl)Al(L) _n P in solutions were determined. The influence of the nature of the macrocyclic ligand and organic base on the coordination properties of aluminum porphyrinate was observed. The degree of deformation of the metalloporphyrin and its molecular complexes was estimated. A good correlation between the experimental and calculated characteristics     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Polarizable empirical force field for nitrogen‐containing heteroaromatic compounds based on the classical Drude oscillator

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen‐containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole, and purine. Initial parameters for the six‐membered rings were based on benzene with nonbond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of five‐member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data were used for the determination of initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard‐Jones (LJ) parameters, through computations of the interactions of dimers of model compounds, model compound‐water interactions, and interactions of rare gases with model compounds. The absolute values of the LJ parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters, and free energies of hydration. Final scaling of the polarizabilities from the gas‐phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities, and isothermal compressibilities, including data as a function of temperature. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Bonding properties of copper(II)—N chromophores: Preparation,structure, and spectroscopic properties of ethylenediaminecopper(II) complexes. Molecular structure of [Cu(ethylenediamine)(pyridine)2(ClO4)2]

Summary Ethylenediaminecopper(II) perchlorate complexes of the [Cu(ethylenediamine)L₂(ClO₄)₂] type, where L = imidazole, N-methylimidazole, 2-methylimidazole, 4-methylimidazole, and pyridine, have been prepared and characterized by elemental analyses, and electronic, vibrational, and e.p.r. spectroscopic measurements. The molecular structure of [Cu(ethylenediamine)(pyridine)₂(ClO₄)₂] has been determined by three-dimensional X-ray diffraction data. The Cu^II ion is coordinated by one ethylenediamine and two pyridine ligands forming an equatorial plane, and by two perchlorate anions located on the z axis. The pyridine ligands incline at 54.9 ° to the CuN₄ plane suggesting virtually no -interaction in the complex. Similar structures with a CuN₄ coordination plane are proposed for other complexes based on the spectroscopic data. The bonding properties of these complexes are elucidated and discussed with reference to the electronic structures deduced from Gaussian analyses of their LF spectra.     

Structure of the Complex of [Ru(tpm)(dppz)py]2+ with a B‐DNA Oligonucleotide—A Single‐Substituent Binding Switch for a Metallo‐Intercalator

We report the synthesis of three new complexes related to the achiral [Ru(tpm)(dppz)py]²⁺ cation (tpm=tripyridazole methane, dppz=dipyrido[3,2‐a:2′,3′‐c]phenazine, py=pyridine) that contain an additional single functional group on the monodentate ancillary pyridyl ligand. Computational calculations indicate that the coordinated pyridyl rings are in a fixed orientation parallel to the dppz axis, and that the electrostatic properties of the complexes are very similar. DNA binding studies on the new complexes reveal that the nature and positioning of the functional group has a profound effect on the binding mode and affinity of these complexes. To explore the molecular and structural basis of these effects, circular dichroism and NMR studies on [Ru(tpm)(dppz)py]Cl₂ with the octanucleotides d(AGAGCTCT)₂ and d(CGAGCTCG)₂, were carried out. These studies demonstrate that the dppz ligand intercalates into the G²–A³ step, with {Ru(tpm)py} in the minor groove. They also reveal that the complex intercalates into the binding site in two possible orientations with the pyridyl ligand of the major conformer making close contact with terminal base pairs. We conclude that substitution at the 2‐ or 3‐position of the pyridine ring has little effect on binding, but that substitution at the 4‐position drastically disrupts intercalative binding, particularly with a 4‐amino substituent, because of steric and electronic interactions with the DNA. These results indicate that complexes derived from these systems have the potential to function as sequence‐specific light‐switch systems.     

DNA Binding and Cleavage Activity of cis‐Cobalt Aromatic Oxime Complexes and Its Pyridine/imidazole Adducts

cis‐Cobalt complexes with salicycaldoxime(SAO), (Z)‐1‐(2‐hydroxyphenyl)ethanonoxime (HEO), (Z)‐1‐(2,5‐dihydroxyphenyl)ethanonoxime (DEO), (Z)‐1‐(2,5‐dihydroxyphenyl)(phenyl)methanonoxime (DPO) and their adducts with pyridine (Py) and imidazole (Im) were synthesized and characterized by elemental analysis, magnetic susceptibility, UV‐Vis and IR spectra. The electrochemical studies were carried by cyclic voltammeter, the peak potential separation and formal potential of complexes were independent of sweep rate or scan rate (ν) indicating a quasi reversible one‐electron redox process. Absorption studies and thermal denature studies revealed that each of these octahedral complexes is an avid binder of calf thymus DNA. The apparent binding constants for mixed ligand complexes are in order of ～10³‐10³ M^?1. Based on the data obtained in the DNA binding studies a partial intercalative mode of binding is suggested for these complexes. The nucleolytic cleavage activity of parent complexes and their pyridine adduct were carried out on double stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment in the presence and absence of oxidant (H₂O₂). All the metal complexes show enhanced cleavage activity in presence of oxidant. The hydrolytic cleavage of DNA of Co(DEO)₂ and Co(DPO)₂ is evidenced from the control experiments showing discernable cleavage inhibition in the presence of the hydroxyl radical inhibitor DMSO and EDTA.     

13C, 14N, 15N and 17O NMR spectra of nitropyrroles and nitroimidazoles

Carbon, nitrogen and oxygen NMR spectra of some nitro derivatives of pyrrole and imidazole have been investigated. The ¹³C chemical shifts of para-carbons and the ¹⁷O chemical shifts of the nitro group correlate qualitatively with the electron densities on these carbon and oxygen atoms, which in turn depend upon the degree of conjugation of the nitro groups with the heterocyclic ring. Conjugation of several nitro groups with the benzene ring is in most cases not impaired by mutual interactions and the ¹³C shifts show good additivity. Such additivity is much worse in pyrrole and imidazole derivatives. Taken together with the diamagnetic nature of these deviations from additivity, this leads to a possible conclusion about the less pronounced conjugation of the nitro groups with the heterocyclic ring in heterocyclic dinitro derivatives.     

Theoretical study on the adsorption of aromatic compounds on platinum clusters

B3 LYP hybrid functional with LACVP* pseudopotential was applied for the optimization of geometries of complexes resulting from interaction of benzene, pyridine, naphthalene, and quinoline with Pt_n (n = 4, 7) clusters. For benzene‐containing complexes, the most stable form corresponds to a bridge adsorption, with benzene undergoing considerable geometric distortions, assuming a boat‐like conformation. C? H bonds are bended upward from the plane of the cluster. C? C bonds stretch, especially when they form π‐complexes with low coordinated Pt atoms. Some arrangements for pyridine complexes involving the N atom of the organic moiety undergo further distortions, apparently preserving a formal C? N π bond. Except for that distortion, the behavior of any heteroaromatic complex is similar to that of benzene in the same arrangement. The quinoline–Pt₇ complex can suitably be used for simulation of the cinchonidine (CD) anchorage over Pt. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Models for Copper-Dioxygen Complexes: The chemistry of copper(II) with some planar tridentate nitrogen ligands

The solution chemistry of Cu(II) with a series of five planar tridentate nitrogen ligands, 2,6-bis(benzimidazol-2-yl)pyridine (bzimpy, 1 ), 2,6-bis(l-methylbenzimidazol-2-yl)pyridine (mbzimpy, 2 ) 2,6-bis(benzothiazol-2-yl) pyridine (bzthpy, 3 ), 2,6-bis(benzoxazol-2-yl)pyridine (bzoxpy, 4 ), and 2,2′, 6′, 2″-terpyridyl (terpy, 5 ) is reported. Electronic and EPR spectra are consistent with the complexes [CuL]²⁺ having essentially tetragonal structure in solution, with the fourth coordination site in the plane of the ligand occupied by solvent. bzthpy and bzoxpy show smaller ligand-field splittings than bzimpy, mbzimpy, and terpy, and are easily decomplexed from the copper. Substitution of the coordinated solvent molecule in the plane of the ligand is observed with Cl^? and OH^? (provided that the ligand has no acidic protons) for all ligands except terpy. The reaction between [Cu(mbzimpy)]²⁺ and imidazole has been studied by potentiometric titration in MeCN/H₂O 1:1 and shows strong binding of the imidazole in the plane (log K = 4.5 at 25°), and also the formation of an imidazolate-bridged dinuclear species.     

Ab initio study of the π–π interactions between CO2 and benzene,pyridine, and pyrrole

The π–π interactions between CO₂ and three aromatic molecules, namely benzene (C₆H₆), pyridine (C₅H₅N), and pyrrole (C₄H₅N), which represent common functional groups in metal‐organic/zeoliticimidazolate framework materials, were characterized using high‐level ab initio methods. The coupled‐cluster with single and double excitations and perturbative treatment of triple excitations (CCSD(T)) method with a complete basis set (CBS) was used to calibrate Hartree–Fock, density functional theory, and second‐order M?ller–Plesset (MP2) with resolution of the identity approximation calculations. Results at the MP2/def2‐QZVPP level showed the smallest deviations (only about 1 kJ/mol) compared with those at the CCSD(T)/CBS level of theory. The strength of π–π binding energies (BEs) followed the order C₄H₅N > C₆H₆ ～ C₅H₅N and was roughly correlated with the aromaticity and the charge transfer between CO₂ and aromatic molecule in clusters. Compared with hydrogen‐bond or electron donor–acceptor interactions observed during BE calculations at the MP2/def2‐QZVPP level of theory, π–π interactions significantly contribute to the total interactions between CO₂ and aromatic molecules. © 2013 Wiley Periodicals, Inc.     

Interpretation of the Electronic Spectra of Ruthenium Nitrosyl Complexes with Nitrogen-containing Heterocyclic Ligands

The electronic absorption spectra of ruthenium nitrosyl complexes with nitrogen-containing heterocyclic ligands were analyzed on the basis of ab initio and CINDO/CI semiempirical calculations of free ligands L and complexes trans-[Ru(NO)(NH₃)₄(L)]^{3 +} (L = pyridine, pyrazine, nicotinamide, isonicotinamide, l-histidine, imidazole). Spectral manifestations of a strong covalent Ru-NO bond were observed to conclude that the oxidation states of Ru and NO in the RuNO^{3 +} group are expedient to represent as Ru(III) and NO⁰. Introduction of a nitrosyl group into the inner coordination sphere of Ru(II) complexes with nitrogen-containing heterocyclic ligands much affects the entire spectral patterns and denudes these ligands of the capacity to exhibit chromophoric properties.     

Isotropic NMR Shifts in Imidazole, 2-Methyl Imidazole and n-Methyl Imidazole Complexed with Copper (II) β-Diketonates

Isotropic nuclear magnetic resonance shifts have been measured for imidazole (Im), 2-methyl imidazole (2MeIm) and N-methyl imidazole (NMeIm) adducts with Cu(AA)₂, Cu(TFA), and Cu(HFA)₂, where AA, TFA and HFA are anion of acetylacetone, trifluoroacetylacetone and hexafluoroacetylacetone, respectively, in deuteriochloroform solution. The pseudocontact contribution to the isotropic shifts are negligibly small and Ferrmi contact interaction is dominant in these copper complexes. The normal temperature effect and appreciable spin delocalization suggest that the imidazole and substituted imidazole adducts with Cu(chelate)₂ are all six-coordinated octahedral complexes, and consistent with our results of spectrophotometric study. In these imidazole complexes, the magnitude of the contact shifts lie in the order Cu(HFA)₂>Cu(TFA)₂>Cu(AA)₂, which is the same as that of the stability constants for the pyridine type adduct formation found from spectrophotometric studies. For a given Cu(chelate)₂, the basicity of ligand for adduct formation is in the order NMeIm>Im>2MeIm.     

Computational Study of the Interactions between Benzene and Crystalline Ice Ih: Ground and Excited States

Ground‐state geometries of benzene on crystalline ice cluster model surfaces (I_h) are investigated. It is found that the binding energies of benzene‐bound ice complexes are sensitive to the dangling features of the binding sites. We used time‐dependent DFT to study the UV spectroscopy of benzene, ice clusters, and benzene–ice complexes, by employing the M06‐2X functional. It is observed that the size of the ice cluster and the dangling features have minor effects on the UV spectral characteristics. Benzene‐mediated electronic excitations of water towards longer wavelengths (above 170 nm) are noted in benzene‐bound ice clusters, where the cross‐section of photon absorption by water is negligible, in good agreement with recent experimental results (Thrower et al., J. Vac. Sci. Technol. A, 2008, 26 , 919–924). The intensities of peaks associated with water excitations in benzene–ice complexes are found to be higher than in isolated ice clusters. The π→π* electronic transition of benzene in benzene–ice complexes undergoes a small redshift compared with the isolated benzene molecule, and this holds for all benzene‐bound ice complexes.     

Transferable potentials for phase equilibria. 9. Explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds

The explicit hydrogen version of the transferable potentials for phase equilibria (TraPPE-EH) force field is extended to benzene, pyridine, pyrimidine, pyrazine, pyridazine, thiophene, furan, pyrrole, thiazole, oxazole, isoxazole, imidazole, and pyrazole. While the Lennard-Jones parameters for carbon, hydrogen (two types), nitrogen (two types), oxygen, and sulfur are transferable for all 13 compounds, the partial charges are specific for each compound. The benzene dimer energies for sandwich, T-shape, and parallel-displaced configurations obtained for the TraPPE-EH force field compare favorably with high-level electronic structure calculations. Gibbs ensemble Monte Carlo simulations were carried out to compute the single-component vapor-liquid equilibria for benzene, pyridine, three diazenes, and eight five-membered heterocycles. The agreement with experimental data is excellent with the liquid densities and vapor pressures reproduced within 1 and 5%, respectively. The critical temperatures and normal boiling points are predicted with mean deviations of 0.8 and 1.6%, respectively.     

ReviewInverse coordination. Organic nitrogen heterocycles as coordination centers. A survey of molecular topologies and systematization. Part 1. Five-membered and smaller rings

Abstract

This review continues the previous articles (I. Haiduc, J. Coord. Chem., 71, 3139 (2018) and J. Coord. Chem., 72, 35 (2019)), which discussed the structures with nitrogen-donor species (atoms and molecules) acting as centers in inverse coordination complexes. i.e. metal compounds which display an arrangement of acceptor and donor sites opposite to that occurring in conventional coordination complexes. This review is Part 1 of a work which introduces the topology of inverse coordination complexes with organic nitrogen heterocycles, and presents a panorama of five-membered rings and covers pyrazole, imidazole, triazoles, tetrazole, pyrrole, oxadiazole, thiadiazole, azaphospholes, and smaller rings.     

Molecular Complexes of Phthalocyanine with Organic Solvents

It was established that in crystal solvates and solutions zinc(II)tetra-tert-butylphthalocyanine formed stable molecular complexes with benzene and pyridine. The characteristics of the corresponding molecular complexes were estimated. Molecules of electron-donor and aromatic solvents do not break down the zinc(II)tetra-tert-butylphthalocyanine associates and do not facilitate intraphase polymorphic transition. A comparative analysis was carried out for the coordinative properties of zinc(II)tetra-tert-butylphthalocyanine and its structural analog, zinc(II)tetrabenzoporphyrin, with respect to pyridine in benzene solutions.     

Specific ion-molecule interactions of imidazole and 1-methylimidazole in nitrobenzene

We have studied, by conductivity measurements, the formation of hydrogenbonded complexes between imidazoles and ions in the three systems triethylammonium picrate (Et₃NHPic)+imidazole (Im), triethylammonium bromide (Et₃NHBr)+Im, and Et₃NHPic+1-methylimidazole (1-MeIm) in nitrobenzene in order to specify the importance of the two functions of the imidazole molecule, the tertiary nitrogen N₃, and the imino group N₁-H. While 1-MelIm forms only a single complex with the cationic species Et₃NH⁺, imidazole enters into specific interactions as well with the cations through its basic site N₃ and with the anions through its imino group. The complexing of the anions by imidazole, always weaker than the complexing of the cations, is more effective for Br^– than for Pic^–. Moreover, if imidazole is used as ligand, a 1:2 complex is formed between the cation and the imidazole, in which the second molecule of imidazole is bonded to the N-H group of the first by a hydrogen bond at the tertiary N atom. We did not observe a correlation between the equilibrium constants K ₁ ⁺ for the complexing of the cation Et₃NH⁺ by imidazole and pyridines (k ₁ ⁺ for pyridine, 3–4 dimethylpyridine, and imidazole are 8, 24, and 165, respectively) and the pK _a values of these ligands due to the fundamental difference in the structure of the imidazole and pyridine molecules, although both are considered as aromatic nitrogen bases.     

Coordination properties of bidentate (N,O) and tridentate (N,O,O) heterocyclic alcohols with dimethyltin(IV)

The complex-formation equilibria of dimethyltin(IV) (DMT) with 4-hydroxymethyl imidazole (HMI) and 2,6-dihydroxymethyl pyridine (PDC) have been investigated. Stoichiometry and stability constants for the complexes formed were determined at different temperatures and 0.1?mol?L^?1 NaNO₃ ionic strength. The concentration distribution of the complexes in solution was evaluated as a function of pH. The effect of dioxane as a solvent on both protonation constants and formation constants of DMT complexes with HMI and PDC are discussed. The thermodynamic parameters ΔH° and ΔS° calculated from the temperature dependence of the equilibrium constants were investigated.     

N-isopropenylazoles: III. Quantum-chemical analysis of the reaction of azoles with allene and propyne in the gas phase

Reactions of pyrrole, imidazole, pyrazole, and 1,2,4-triazole with allene and propyne in the gas phase with formation of the corresponding N-isopropenylazoles were simulated at the RHF/6-31G**, B3LYP/6-31G**, and MP2(full)/6-31G** levels. Dissociation of the N-H bond to give azolate ion is the main constituent of the reaction coordinate. All the examined azoles react preferentially with allene rather than with propyne; their reactivity decreases in the series pyrrole > imidazole > pyrazole > 1,2,4-triazole due to participation of the pyridine type nitrogen atoms in the prototropic propyne-allene rearrangement.