Contribution to the Protonation of a Calix[4]arene: DFT Calculated Structure of Protonated p-tert -Butylcalix[4]arenetetrakis( N , N -diethylacetamide)

By using DFT calculations, the most probable structure of the p-tert-butylcalix[4]arenetetrakis(N,N-diethylacetamide) · H₃O⁺ complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is predominantly bound by strong hydrogen bonds to three phenoxy oxygens of the ligand and partly to the remaining phenoxy oxygen atom by two somewhat weaker hydrogen bonds. Besides, the H₃O⁺ cation is also bound to two carbonyl oxygens of the mentioned ligand by further two weaker hydrogen bonds.     

Theoretical study on the protonation of cucurbit[6]uril

Abstract  

The most probable structures of the cucurbit[6]uril·H₃O⁺ and cucurbit[6]uril·(H₃O⁺)₂ cationic complex species have been derived by quantum mechanical DFT calculations. In these two complexes, each of the H₃O⁺ ions is bound by three strong linear hydrogen bonds to three carbonyl oxygen atoms of the parent macrocycle.     

Contribution to the Protonation of a Calix[4]arene: DFT Calculated Structure of Protonated <Emphasis Type="Italic">p-tert</Emphasis>-Butylcalix[4]arenetetrakis(<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-diethylacetamide)

Summary. By using DFT calculations, the most probable structure of the p-tert-butylcalix[4]arenetetrakis(N,N-diethylacetamide) · H₃O⁺ complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is predominantly bound by strong hydrogen bonds to three phenoxy oxygens of the ligand and partly to the remaining phenoxy oxygen atom by two somewhat weaker hydrogen bonds. Besides, the H₃O⁺ cation is also bound to two carbonyl oxygens of the mentioned ligand by further two weaker hydrogen bonds.     

DFT-calculated structure of protonated tetraphenyl p - tert -butylcalix[4]arene tetraketone

Using DFT calculations, two of the most probable structures (A, B) of the tetraphenyl p-tert-butylcalix[4]arene tetraketone·H₃O⁺ cationic complex species were derived. The hydroxonium ion H₃O⁺, placed in the coordination cavity formed by the calix[4]arene lower-rim groups, is bound by strong hydrogen bonds to the phenoxy oxygen atoms of the calix[4]arene ligand (structures A, B) and also to one carbonyl oxygen (structure B).     

DFT-calculated structure of protonated tetraphenyl <Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">tert</Emphasis>-butylcalix[4]arene tetraketone

Using DFT calculations, two of the most probable structures (A, B) of the tetraphenyl p-tert-butylcalix[4]arene tetraketone·H₃O⁺ cationic complex species were derived. The hydroxonium ion H₃O⁺, placed in the coordination cavity formed by the calix[4]arene lower-rim groups, is bound by strong hydrogen bonds to the phenoxy oxygen atoms of the calix[4]arene ligand (structures A, B) and also to one carbonyl oxygen (structure B). Correspondence: Emanuel Makrlík, Faculty of Applied Sciences, University of West Bohemia, Pilsen, Czech Republic.     

Theoretical study on the protonation of bambus[6]uril

Abstract  

Quantum mechanical density functional theory (DFT) calculations were used to derive the most probable structures of the bambus[6]uril·H₃O⁺ and bambus[6]uril·(H₃O⁺)₂ cationic complex species. In these two complexes, each of the considered H₃O⁺ ions is bound by three strong linear hydrogen bonds to the three corresponding carbonyl oxygens of the parent macrocyclic receptor.     

Experimental evidence, stability, and the most probable structure of protonated p-tert-butylcalix[4]arenetetrakis(N,N-dimethylacetamide)

Abstract  

From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium H₃O⁺(aq) + 1·Na⁺(nb) \leftrightarrows \leftrightarrows 1·H₃O⁺ (nb) + Na⁺ (aq) taking place in the two-phase water–nitrobenzene system (1 = p-tert-butylcalix[4]arenetetrakis(N,N-dimethylacetamide); aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log K _ex (H₃O⁺, 1·Na⁺) = −0.1 ± 0.1. Further, the stability constant of the 1·H₃O⁺ complex in water-saturated nitrobenzene was calculated for a temperature of 25 °C as log β _nb (1·H₃O⁺) = 10.9 ± 0.2. By using quantum mechanical DFT calculations, the most probable structure of the 1·H₃O⁺ cationic complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is bound partly to one phenoxy oxygen atom and partly to two carbonyl oxygens of 1 by strong hydrogen bonds and obviously by other electrostatic interactions.     

Experimental Evidence for Unusual Protonation of Tetraethyl p-tert-Butylcalix[4]arene Tetraacetate and the Most Probable Structure of the Resulting Complex

Using ¹H and ¹³C NMR, FT IR spectroscopy together with quantum mechanical DFT calculations, we show that tetraethyl p-tert-butylcalix[4]arene tetraacetate (1) forms a stable equimolecular complex with proton in the form of hydroxonium ion in acetonitrile-d ₃. Protons for this complex were offered by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and converted to hydroxonium ions by traces of water. The complex 1·H₃O⁺ adopts a slightly asymmetric conformation, which is distinctly more cone-like than ligand 1. According to spectral evidence, the hydroxonium ion H₃O⁺ is bound mainly to three of the phenoxy oxygen atoms of 1 by strong hydrogen bonds leaving the ester carbonyl groups, which are the usual coordination site for metal cations, free. Theoretical DFT calculations support the bonding to phenoxy oxygen atoms but slightly prefer a structure with one of the carbonyls being involved in the coordination.     

A Proton Complex of p-tert-Butylcalix[4]arene-tetrakis(N,N-dimethylthioacetamide): NMR Evidence and Probable Structure

Using ¹H and ¹³C NMR together with density functional theoretical (DFT) calculations, it is shown that p-tert-butylcalix[4]arene-tetrakis(N,N-dimethylthioacetamide) (1) forms a stable equimolecular complex with proton in the form of hydroxonium ion in nitrobenzene-d ₅. Protons were offered by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and converted to hydroxonium ions by traces of water. The complex 1·H₃O⁺ adopts a slightly asymmetric but rapidly motionally averaged conformation, which is distinctly more cone-like than ligand 1. The hydroxonium ion H₃O⁺ is bound partly to thiocarbonyl sulphur atoms and partly to phenoxy oxygen atoms of 1 by strong hydrogen bonds and other electrostatic interactions.

     

Extraction and DFT study on the complexation of H3O+ ion with tetrakis(2-ethoxyethoxy)-tetra-p-tert-butylcalix[4]arene

Abstract  

Extraction experiments in the two-phase water/nitrobenzene system and γ-activity measurements were used to determine the stability constant of protonated tetrakis(2-ethoxyethoxy)-tetra-p-tert-butylcalix[4]arene in nitrobenzene saturated with water. Density functional theory (DFT) calculations were applied to derive the most probable structure of the tetrakis(2-ethoxyethoxy)-tetra-p-tert-butylcalix[4]arene·H₃O⁺ complex species.     

Protonation of Tetrapropoxy-4-tert-butylcalix[4]arene: NMR Study of Interaction and Probable Structures of the Product

Using ¹H and ¹³C NMR spectroscopy, the interaction of tetrapropoxy-p-tert-butyl-calix[4]arene (1) with H₃O⁺ ions produced by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and traces of water was studied in nitrobenzene-d ₅. It was shown that 1 readily forms an equimolecular complex with H₃O⁺. The equilibrium constant K of its formation is 2.6 at 296 K. Exchange between bound and free 1 is fast even under mild excess of HDCC, the correlation time τ_ex being about 0.13 ms. NMR shows that H₃O⁺ is bound to the aryl-oxygen atoms and this binding forces the calixarene cup to adopt a more open and symmetrical conformation. This conclusion is in full accord with high precision quantum DFT calculations which find one structure of the complex corresponding to a global energy minimum, in which the H₃O⁺ ion is bound to three of the oxygen atoms by strong hydrogen bonds and to the remaining oxygen by two weaker hydrogen bonds. The calixarene part is forced into a C₄ symmetrical opened form.

When stored for weeks, the complex gradually transforms into other forms, most probably its hydrates, according to spectral evidence and DFT calculations.     

Synthesis and crystal structure of a supramolecular adduct of trinuclear molybdenum oxocluster with macrocyclic cavitand cucurbit[5]uril containing the included ionic associate Na<Superscript>+</Superscript>...Cl...Na<Superscript>+</Superscript>

The compound of composition [{Mo₃O₄(H₂O)₆Cl₃}₂(Na₂Cl⊂ C₃₀H₃₀N ₂₀O₁₀)]Cl₃⋅14H₂O (1) was prepared by evaporation of a hydrochloric acid solution containing NaCl, the trinuclear aqua complex [Mo₃O₄(H₂O)₉]⁴⁺, and the macrocyclic cavitand cucurbit[5]uril (C₃₀H₃₀N₂₀O₁₀). X-ray diffraction analysis demonstrated that the cucurbit[5]uril molecule is closed on both sides by the cluster cations through hydrogen bonding between the CO groups of the cucurbit[5]uril portals and the aqua ligands of the oxo cluster. The inner cavity of the supramolecular adduct includes an unusual ionic associate Na⁺...Cl...Na⁺. The sodium cations are coordinated by five carbonyl oxygen atoms of each portal of the macrocycle. Compound 1 is the first structurally characterized complex, in which the macrocyclic cucurbit[5]uril ligand is directly coordinated to the alkali metal cation. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1513–1517, July, 2005.     

Synthesis, Crystal Structure, Photophysical Properties, and DFT Calculations of a Bis(tetrathia-calix[4]arene) Tetracadmium Complex

Abstract  

Thiacalix[4]arenes are a unique family of polydentate ligands that offer a combination of four soft sulfur atoms together with four hard phenol oxygen atoms for binding to metal ions. In this study, the tetranuclear cadmium (II) complex Cd₄^II(tca)₂·1.5CH₂Cl₂ (tca⁴⁻ = tetra-anionic p-tert-butylthiacalix[4]arene) (1) was synthesized by reaction of a deprotonated p-tert-butylthiacalix[4]arene and various Cd^II salts. The structure of 1 was established by single crystal X-ray diffraction analysis. The neutral complex 1 contains a square arrangement of four cadmium (II) ions sandwiched between two tca⁴⁻ ligands that have a ‘cone’ conformation similar to that of the free ligand. The absorption and emission properties of the free ligand H₄tca and complex 1 have been recorded and explained by DFT calculations of the molecular orbitals and electronic transitions between them.     

Stability constants of the Li+, Na+, H3O+, NH4+, Ag+, and K+ complexes of the cone conformer of tetraethyl p-tert-butyltetrathiacalix[4]arene tetraacetate in nitrobenzene saturated with water

Abstract  

From extraction experiments in the two-phase water–nitrobenzene system and γ-activity measurements, the stability constants of the tetraethyl p-tert-butyltetrathiacalix[4]arene tetraacetate (cone)·M⁺ complexes (M⁺ = Li⁺, H₃O⁺, NH₄ ⁺, Ag⁺, or K⁺) were determined in water-saturated nitrobenzene. It was found that these constants increase in the cation order NH₄ ⁺ < K⁺ < H₃O⁺ < Ag⁺ < Li⁺ < Na⁺.     

Protonation of the acyclic tetraaza metallocomplex of gold(III) [Au(C9H19N4)]2+ in aqueous solution. Synthesis and crystal and molecular structure of [Au(C9H20N4)](H5O2)(ClO4)4

Protonation equilibrium has been studied for the acyclic gold(III) tetraaza metallocomplex [AuB]²⁺ [B = N, N′-bis(2-aminoethyl)-2,4-pentanediiminato(1−)] in aqueous solution. The synthetic procedure is described. The crystal and molecular structure of the protonated form of the [AuHB](H₅O₂)(ClO₄)₄ complex has been determined. Monoclinic crystals with unit cell dimensions a = 11.964(2) Å, b = 13.789(3) Å, c = 15.496(3) Å, β = 109.00(3)°, V = 2417.1(8) ų, Z = 4, ρcalc = 2.243 g/cm³, space group P2₁/n. The structure is built of nearly planar [Au(C₉H₂₀N₄)]³⁺ complex cations, (H₅O₂)⁺ cations, and [ClO₄]⁻ anions. The gold atom coordinates four nitrogen atoms of the ligand, forming a square plane. The six-membered chelate ring of the ligand is protonated at the central β-carbon atom and contains imine C=N bonds. The oxygen atoms of the perchlorate ions are hydrogen bonded to the (H₅O₂)⁺ dihydroxonium ion and to the nitrogen atoms of the NH₂ groups of the [AuHB]³⁺ cation. Original Russian Text Copyright ? 2005 by V. A. Afanasieva, L. A. Glinskaya, R. F. Klevtsova, and I. V. Mironov __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 46, No. 5, pp. 909–915, September–October, 2005.     

Crystal structure of a calcium(II) complex with pyrazine-2,3-dicarboxylate,nitrate and water ligands

The structure of catena-[tris(aquo-O)(nitrato-O,O′)(µ-hydrogen pyrazine-2,3-dicarboxylato-O,N–O′,N′)calcium(II)][tetra(aquo-O)(μ-hydrogen pyrazine-2,3-dicarboxylato-O,N–O′,N′) calcium(I)] nitrate, {Ca[H(2,3-PZDC)](H₃O)₃(NO₃)}{Ca[H(2,3-PZDC)](H₂O)₄}⁺ (NO₃)^?, is composed of molecular ribbons in which calcium atoms are bridged by both N,O-bonding moieties of singly deprotonated ligand molecules. The hydrogen atom donated by one carboxylic group is linked by a short intramolecular hydrogen bond of 2.37 Å to an oxygen atom of the second carboxylic group of the same ligand. Two crystallographically independent Ca(II) ions exhibit different coordination modes. One is coordinated by two bonding moieties of the bridging ligand molecules, three water oxygen atoms and two oxygen atoms of a nitrate ligand. The other calcium ion is chelated by two bonding moieties donated by the bridging ligand molecules and four water oxygen atoms, forming a positively charged assembly with a nitrate anion located nearby. The coordination polyhedron of the first calcium ion is a strongly deformed bicapped pentagonal bipyramid with nine-coordinated atoms; the second calcium ion is also in a strongly deformed pentagonal bipyramid with one apex on one side of the equatorial plane and two apices on the other. Coordinated water oxygen atoms act as donors in a hydrogen-bond network.     

Structure and mechanism of fragmentation of [C2H5O]+

The decomposition reactions of [C₂H₅O]⁺ ions produced by dissociative electron-impact ionization of 2-propanol have been studied, using ¹³C and deuterium labeling coupled with metastable intensity studies. In addition, the fragmentation reactions following protonation of appropriately labeled acetaldehydes and ethylene oxides with [H₃]⁺ or [D₃]⁺ have been investigated. In both studies particular attention has been paid to the reactions leading to [CHO]⁺, [C₂H₃]⁺ and [H₃O]⁺. In both the electron-impact-induced reactions and the chemical ionization systems the fragmentation of [C₂H₅O]⁺ to both [H₃O]⁺ and [C₂H₃]⁺ proceeds by a single mechanism. For each case the reaction involves a mechanism in which the hydrogen originally bonded to oxygen is retained in the oxygen containing fragment while the four hydrogens originally bonded to carbon become indistinguishable. The fragmentation of [C₂H₅O]⁺ to produce [CHO]⁺ proceeds by a number of mechanisms. The lowest energy route involves complete retention of the α carbon and hydrogen while a higher energy route proceeds by a mechanism in which the carbons and the attached hydrogens become indistinguishable. A third distinct mechanism, observed in the electron-impact spectra only, proceeds with retention of the hydroxylic hydrogen in the product ion. Detailed fragmentation mechanisms are proposed to explain the results. It is suggested that the [C₂H₅O]⁺ ions formed by protonation of acetaldehyde or ionization of 2-propanol are produced initially with the structure [CH₃CH?\documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm O}\limits^ + $\end{document}H] (a), but isomerize to [CH₂?CH? \documentclass{article}\pagestyle{empty}\begin{document}$ \mathop {\rm O}\limits^ + $\end{document}H₂] (e) prior to decomposition to [C₂H₃]⁺ or [H₃O]⁺. The results indicate that the isomerization a → e does not proceed directly, possibly because it is symmetry forbidden, but by two consecutive [1,2] hydrogen shifts. A more general study of the electron-impact mass spectrum of 2-propanol has been made and the fragmentation reactions proceeding from the molecular ion have been identified.     

Polymorph of {2‐[(2‐hydroxyethyl)iminiomethyl]phenolato‐κO}dioxido{2‐[(2‐oxidoethyl)iminomethyl]phenolato‐κ3O,N,O′}molybdenum(VI)

A second polymorphic form (form I) of the previously reported compound {2‐[(2‐hydroxyethyl)iminiomethyl]phenolato‐κO}dioxido{2‐[(2‐oxidoethyl)iminomethyl]phenolato‐κ³O,N,O′}molybdenum(VI) (form II), [Mo(C₉H₉NO₂)O₂(C₉H₁₁NO₂)], is presented. The title structure differs from the previously reported polymorph [Głowiak, Jerzykiewicz, Sobczak & Ziółkowski (2003). Inorg. Chim. Acta, 356 , 387–392] by the fact that the asymmetric unit contains three molecules linked by O—H...O hydrogen bonds. These trimeric units are further linked through O—H...O hydrogen bonds to form a chain parallel to the [11] direction. As in the previous polymorph, each molecule is built up from an MoO₂²⁺ cation surrounded by an O,N,O′‐tridentate ligand (O⁻C₆H₄CH=NCH₂CH₂O⁻) and weakly coordinated by a second zwitterionic ligand (O⁻C₆H₄CH=N⁺HC₂H₄OH). All complexes are chiral with the absolute configuration at Mo being C or A. The main difference between the two polymorphs results from the alternation of the chirality at Mo within the chain.     

Tripotassium tris­(oxalato‐κ2O,O′)­aluminate bis(hydrogen peroxide) hydrate,the first example of a cyclic hydrogen‐bonded H2O2 dimer

In addition to associating into cyclic hydrogen‐bonded dimers [O⋯O = 2.663 (1) and 2.914 (1) Å], each hydrogen peroxide mol­ecule in the title structure, K₃[Al(C₂O₄)₃]·1.75H₂O₂·0.25H₂O, hydrogen bonds to a neighbouring oxalate ligand [O⋯O = 2.700 (1) and 2.730 (1) Å] and coordinates to two K⁺ ions [K⋯O = 2.6620 (9)–2.8380 (7) Å].     

Preparation and crystal structure of a 1:4 diaqua(benzo-15-crown-5)(perchlorato-<Emphasis Type="Italic">O</Emphasis>)calcium perchlorate and diaqua(4′-nitrobenzo-15-crown-5)(perchlorato-<Emphasis Type="Italic">O</Emphasis>)calcium perchlorate solid solution

A 1:4 diaqua(benzo-15-crown-5)(perchlorato-O)calcium perchlorate and diaqua(4-nitrobenzo-15-crown-5)(perchlorato-O)calcium solid solution [Ca(ClO₄)LH₂O)₂]⁺ClO ₄ ^– [L = (B15C5)_0.2(4-NO₂-B15C5)_0.8] was prepared and studied by X-ray diffraction. The complex cation [Ca(ClO₄)L(H₂O)₂]⁺ is of the guest-host type. The coordination polyhedron of its Ca²⁺ cation is irregular, viz. a distorted prism with two different bases: pentagonal (of five ether oxygen atoms of mixed crown ligand L) and trigonal (of one oxygen atom of the anionic ligand ClO ₄ ^– and two oxygen atoms of the two water molecules). The packing of the complex cations and disordered ClO ₄ ^– anions in the crystal structure of this solid solution was determined to find that these ions are connected by hydrogen bonds into infinite three-dimensional layers.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 8, 2004, pp. 1244–1249.Original Russian Text Copyright © 2004 by Chekhlov.This revised version was published online in April 2005 with a corrected cover date.